Alex Kid:
Here's an additional suggestion when re-mastering the CD. It's a good idea to retain the original file ordering of the CD when re-creating the ISO from files/folder on your hard drive. What you do is use ISObuster to view the filesystem of the game CD on your CD-ROM drive. Right click on the name of the ISO track, Copy Tree-Info to file, save to your desktop or something (FileList.txt will be generated). Then use a little program called F2S.exe (35KB if compressed with UPX) to change the format of FileList.txt to that of a sort text file to be used when creating the ISO file with MKISOFS.EXE. This method is very useful when the CD has an optimized file ordering (non-alphabetical) and if there are too many files/folders to create the sort text file manually. When running the command line to create the ISO file using MKISOFS, you could Ctrl+C to break after like a few percent is complete and not wait for the whole ISO file to be completely generated. CDmage should allow you to open the partially created (mode 1, 2048) ISO file and view the LBA ordering. Just compare the ordering you see there with the file ordering that you see with ISObuster viewing the CD on your CD-ROM drive. If it checks, run the command line to create the ISO file again, patch the boot sector of the ISO file with IPINS.EXE, then burn to CD. Also, the command line to create the ISO image should look something like this:
mkisofs -V "NINPEN_MANMARU" -l -sort ninpenSort.txt -o data.iso data
ninpenSort.txt would be the name of the sort text file, of course.
If you don't know where to get the F2S.EXE program, I've emailed it to you (39KB).
BTW, I haven't tried out your patch since I don't even have the game to begin with, so I don't know if you've applied the file sort or not in your process of recreating the ISO with the patched files, nor do I know what the file ordering of the original game CD is like.